From 0e535a23456dc79f4e993e28b8ea5caca2125bcc Mon Sep 17 00:00:00 2001
From: ahmedk <karim.ahmed@xfel.eu>
Date: Tue, 20 Feb 2024 15:22:19 +0100
Subject: [PATCH] final changes related by differentiating between module index
and module numbers. This should all be replaced with CALCAT metadata
---
.../AGIPD/AGIPD_Correct_and_Verify.ipynb | 5 ++--
.../Characterize_AGIPD_Gain_Darks_NBC.ipynb | 28 ++++++++++---------
2 files changed, 18 insertions(+), 15 deletions(-)
diff --git a/notebooks/AGIPD/AGIPD_Correct_and_Verify.ipynb b/notebooks/AGIPD/AGIPD_Correct_and_Verify.ipynb
index 888cf41a2..2ac606a4e 100644
--- a/notebooks/AGIPD/AGIPD_Correct_and_Verify.ipynb
+++ b/notebooks/AGIPD/AGIPD_Correct_and_Verify.ipynb
@@ -289,10 +289,11 @@
" if modules[0] == -1:\n",
" modules = list(range(nmods))\n",
" karabo_da = [\"AGIPD{:02d}\".format(i) for i in modules]\n",
- "else:\n",
+ "else: # TODO: fix this with the new CALCAT metadata for module indices.\n",
" modules = [int(x[-2:]) for x in karabo_da]\n",
+ " mod_indices = modules if nmods > 1 else [0]\n",
"\n",
- "print(\"Process modules:\", ', '.join(module_index_to_qm(x) for x in modules))\n",
+ "print(\"Process modules:\", ', '.join(module_index_to_qm(x) for x in mod_indices))\n",
"print(f\"Detector in use is {karabo_id}\")\n",
"print(f\"Instrument {instrument}\")"
]
diff --git a/notebooks/AGIPD/Characterize_AGIPD_Gain_Darks_NBC.ipynb b/notebooks/AGIPD/Characterize_AGIPD_Gain_Darks_NBC.ipynb
index b89a5bccb..3218edf61 100644
--- a/notebooks/AGIPD/Characterize_AGIPD_Gain_Darks_NBC.ipynb
+++ b/notebooks/AGIPD/Characterize_AGIPD_Gain_Darks_NBC.ipynb
@@ -19,21 +19,21 @@
"metadata": {},
"outputs": [],
"source": [
- "in_folder = \"/gpfs/exfel/d/raw/CALLAB/202031/p900113\" # path to input data, required\n",
- "out_folder = \"\" # path to output to, required\n",
+ "in_folder = \"/gpfs/exfel/exp/HED/202430/p900438/raw\" # path to input data, required\n",
+ "out_folder = \"/gpfs/exfel/data/scratch/ahmedk/test/remove/agipd_sm/dark\" # path to output to, required\n",
"metadata_folder = \"\" # Directory containing calibration_metadata.yml when run by xfel-calibrate\n",
"modules = [-1] # list of modules to evaluate, RANGE ALLOWED\n",
- "run_high = 9985 # run number in which high gain data was recorded, required\n",
- "run_med = 9984 # run number in which medium gain data was recorded, required\n",
- "run_low = 9983 # run number in which low gain data was recorded, required\n",
+ "run_high = 1 # run number in which high gain data was recorded, required\n",
+ "run_med = 2 # run number in which medium gain data was recorded, required\n",
+ "run_low = 3 # run number in which low gain data was recorded, required\n",
"operation_mode = \"ADAPTIVE_GAIN\" # Detector operation mode, optional (defaults to \"ADAPTIVE_GAIN\")\n",
"\n",
- "karabo_id = \"HED_DET_AGIPD500K2G\" # karabo karabo_id\n",
- "karabo_da = ['-1'] # a list of data aggregators names, Default [-1] for selecting all data aggregators\n",
+ "karabo_id = \"HED_DET_AGIPD65K1\" # karabo karabo_id\n",
+ "karabo_da = ['AGIPD08'] # a list of data aggregators names, Default [-1] for selecting all data aggregators\n",
"receiver_template = \"{}CH0\" # inset for receiver devices\n",
"instrument_source_template = '{}/DET/{}:xtdf' # path in the HDF5 file to images\n",
"ctrl_source_template = '{}/MDL/FPGA_COMP' # path to control information\n",
- "karabo_id_control = \"HED_EXP_AGIPD500K2G\" # karabo-id for control device '\n",
+ "karabo_id_control = \"HED_DET_AGIPD65K1\" # karabo-id for control device '\n",
"\n",
"use_dir_creation_date = True # use dir creation date as data production reference date\n",
"cal_db_interface = \"tcp://max-exfl-cal001:8020\" # the database interface to use\n",
@@ -170,7 +170,9 @@
" modules = list(range(nmods))\n",
" karabo_da = create_karabo_da_list(modules)\n",
"else:\n",
+ " # TODO: use CALCAT metadata for detector's modules indices.\n",
" modules = [int(x[-2:]) for x in karabo_da]\n",
+ " mod_indices = modules if nmods > 1 else [0]\n",
"\n",
"print(f\"Detector in use is {karabo_id}\")\n",
"print(f\"Instrument {instrument}\")\n",
@@ -383,7 +385,7 @@
"print(f\"Will use {parallel_num_procs} processes with {parallel_num_threads} threads each\")\n",
"\n",
"def characterize_module(\n",
- " channel: int, gain_run: Tuple[int, int],\n",
+ " mod_index: int, channel: int, gain_run: Tuple[int, int],\n",
") -> Tuple[int, int, np.array, np.array, np.array, np.array, np.array]:\n",
"\n",
" gain_index, run = gain_run\n",
@@ -464,7 +466,7 @@
" bp[(noise < local_thresholds_noise_hard[0]) | (noise > local_thresholds_noise_hard[1])] |= BadPixels.NOISE_OUT_OF_THRESHOLD\n",
" bp[~np.isfinite(noise)] |= BadPixels.OFFSET_NOISE_EVAL_ERROR\n",
"\n",
- " return channel, gain_index, offset, noise, gains, gains_std, bp"
+ " return mod_index, gain_index, offset, noise, gains, gains_std, bp"
]
},
{
@@ -477,7 +479,7 @@
"\n",
"with multiprocessing.Pool(processes=parallel_num_procs) as pool:\n",
" results = pool.starmap(\n",
- " characterize_module, itertools.product(modules, list(enumerate(run_numbers))))\n",
+ " characterize_module, itertools.product(mod_indices, modules, list(enumerate(run_numbers))))\n",
"\n",
"step_timer.done_step(\"Processing dark from the 3 runs.\")\n",
"\n",
@@ -572,7 +574,7 @@
"outputs": [],
"source": [
"res = OrderedDict()\n",
- "for i in modules:\n",
+ "for i in mod_indices:\n",
" qm = module_index_to_qm(i)\n",
" res[qm] = {\n",
" 'Offset': offset_g[qm],\n",
@@ -618,7 +620,7 @@
" snapshot_at=creation_time.isoformat() if creation_time else None,\n",
" timeout=cal_db_timeout\n",
")\n",
- "for module_index, module_da, module_pdu in zip(modules, karabo_da, all_pdus):\n",
+ "for module_index, module_da, module_pdu in zip(mod_indices, karabo_da, all_pdus):\n",
" qm = module_index_to_qm(module_index)\n",
" qm_dict[qm] = {\n",
" \"karabo_da\": module_da,\n",
--
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